If you must store annotations in the repo (for any reason) then checkout,
remove them, code and refactor without annotations, add them back and commit.
Alternatively checkout, code and refactor (ignoring annotations), rebuild them and commit.

For short forms it does not need to see the declaration of myMod so you can run it
on your individual source files without concatenating. If ng-annotate detects a short form
false positive then you can use the --regexp option to limit the module identifier.
Examples: --regexp "^myMod$" (match only myMod) or --regexp "^$" (ignore short forms).